/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2020 UniPro <ugene@unipro.ru>
 * http://ugene.net
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
 * MA 02110-1301, USA.
 */

#include "BlastPPlusSupportTask.h"

#include <QDomDocument>
#include <QFileInfo>

#include <U2Core/AppContext.h>
#include <U2Core/AppResources.h>
#include <U2Core/AppSettings.h>
#include <U2Core/CreateAnnotationTask.h>
#include <U2Core/DocumentModel.h>
#include <U2Core/ExternalToolRegistry.h>
#include <U2Core/Log.h>
#include <U2Core/ProjectModel.h>
#include <U2Core/UserApplicationsSettings.h>

#include "BlastPlusSupport.h"

namespace U2 {

ExternalToolRunTask *BlastPPlusSupportTask::createBlastPlusTask() {
    QStringList arguments;
    //arguments <<"-p"<< settings.programName; //taskname
    //    if(!settings.filter.isEmpty()){
    //        arguments <<"-F"<<settings.filter;
    //    }
    arguments << "-db" << settings.databaseNameAndPath;
    arguments << "-evalue" << QString::number(settings.expectValue);
    //    arguments <<"-task"<< (settings.megablast ? "megablast" : "blastn");
    if (settings.wordSize <= 0) {
        arguments << "-word_size"
                  << "3";
    } else {
        arguments << "-word_size" << QString::number(settings.wordSize);
    }
    if (!settings.isDefaultCosts) {
        arguments << "-gapopen" << QString::number(settings.gapOpenCost);
        arguments << "-gapextend" << QString::number(settings.gapExtendCost);
    }
    if (settings.isNucleotideSeq && (!settings.isDefautScores)) {
        assert(false);
        arguments << "-penalty" << QString::number(settings.mismatchPenalty);
        arguments << "-reward" << QString::number(settings.matchReward);
    } else {
        if (!settings.isDefaultMatrix) {
            arguments << "-matrix" << settings.matrix;
        }
    }
    if (settings.numberOfHits != 0) {
        arguments << "-culling_limit" << QString::number(settings.numberOfHits);    //???
    }
    if (!settings.isGappedAlignment) {
        arguments << "-ungapped";
    }

    arguments << "-query" << url;

    if (settings.xDropoffGA != 15) {
        arguments << "-xdrop_gap" << QString::number(settings.xDropoffGA);
    }
    if (settings.xDropoffFGA != 25) {
        arguments << "-xdrop_gap_final" << QString::number(settings.xDropoffFGA);
    }

    if (settings.xDropoffUnGA != 7) {
        arguments << "-xdrop_ungap" << QString::number(settings.xDropoffUnGA);
    }
    if (!settings.isDefaultThreshold) {
        arguments << "-threshold" << QString::number(settings.threshold);
    }
    if (settings.windowSize != 40) {
        arguments << "-window_size" << QString::number(settings.windowSize);
    }
    if (settings.programName == "gpu-blastp") {
        arguments << "-gpu"
                  << "t";
    }
    if (!settings.compStats.isEmpty()) {
        arguments << "-comp_based_stats" << settings.compStats;
    }
    arguments << "-num_threads" << QString::number(settings.numberOfProcessors);
    arguments << "-outfmt" << QString::number(settings.outputType);    //"5";//Set output file format to xml
    if (settings.outputOriginalFile.isEmpty()) {
        arguments << "-out" << url + ".xml";
        settings.outputOriginalFile = url + ".xml";
    } else {
        arguments << "-out" << settings.outputOriginalFile;
    }

    algoLog.trace("BlastP+ arguments: " + arguments.join(" "));
    QString workingDirectory = QFileInfo(url).absolutePath();
    ExternalToolRunTask *runTask = new ExternalToolRunTask(BlastPlusSupport::ET_BLASTP_ID, arguments, new ExternalToolLogParser(), workingDirectory);
    setListenerForTask(runTask);
    return runTask;
}
}    // namespace U2
